Structure Modification Tool
The structure modification tool can be used to change substituents, swap ligands on a organometallic catalyst, attach a ring, or change an element. When changing a substituent or closing a ring, you can change the name of modified residues.
Anything in the AaronTools library or your personal library can be used. You can see what's in the AaronTools libraries and your personal libraries with the Browse AaronTools Libraries tool. The AaronTools substituent and ligand libraries can also be found online. Items can be added to your personal library using the Add to Personal Library tool.
Switch to the 'substitute' tab of the tool.
To change a substituent, you can select the atom on the substituent that is connected to the rest of the molecule. If the 'guess previous substituent' box is checked, the molecule is assumed to be the largest fragment bonded to this substituent atom. If the 'guess previous substituent' box is unchecked, select the rest of the substituent you are replacing. A structure can be edited at multiple positions at once by selecting more than one substituent or atom.
Select the new substituent using its name in the library. You can click the 'from library...' button to pull up a list of substituents in the library. Selecting an item on the list will also populate the substituent name box on the main tool.
If you are concerned about steric clashing with the new substituent, check the 'relax substituent' box. This will rotate the new substituent to reduce clashing.
By default, atom names are the element symbol and a number (e.g., C1, H7). In some cases, particularly protein side chains, it is preferable to name atoms by how far they are from another atom with names like CA, CB, CG, and so on. SEQCROW will attempt to use this naming scheme when you check the 'use distance names' box. Note that the names are determined on-the-fly, so check to make sure they are proper.
To create a copy of the structure with the modified substituent instead of changing the original structure, uncheck the 'modify selected structure' box. This will also allow you generate many different structures with different substituents at once. Substituent names can be separated by commas, and a new copy of the structure will be created for each substituent.
The name of residues can be changed when a substituent is changed by filling in the 'new residue name' box. Residue names should be alphanumeric and no more than 4 characters long. If the 'modify selected structure' box is also unchecked, names can be comma-separated like substituent names to rename the residue in each copy of the structure.
To complete the substituent change, click the 'substitute current selection' button.
Switch to the 'swap ligand' tab of the tool.
To swap a ligand (on an organometallic- or organocatalyst), select the atoms on the ligand that are coordinated to the catalyst center. Next, enter the name of the ligand from the library that you would like to place on your structure. Click the 'from library...' button to pull up a list of ligands in the library. Selecting items on the list will fill in the 'ligand name' box.
If the 'modify selected structure' box is unchecked, a copy of the structure will be created and the new ligand will be placed on it, leaving the original structure unchanged. Also, ligand names can be comma-separated to generate several structures with various ligands.
Clicking the 'swap ligand with selected coordinating atoms' button will replace the ligand.
Ligands can also be dropped into existing structures or a new structure by selecting a model on the drop-down menu and pressing the 'place in' button.
Switch to the 'fuse ring' tab of the tool.
Select two atoms to which the ring will be attached. The ring will contain atoms along the path between these two atoms, supplemented by atoms from the ring in the library. Enter a ring name from the ring library. To pull up a list of rings in the library, click the 'from library...' button. Selecting an item on the list will also populate the 'ring name' on the main tool window.
If there are multiple versions of the ring in the library (e.g., cyclohexane and cyclohexane.1), checking the "try multiple" will ensure all versions of the ring are tried and the best one is used.
To create a copy of the structure with the ring attached, uncheck the 'modify selected structure' box. Multiple copies with different rings can be created by separating ring names with commas. The name of the residue to which the ring is being attached can be changed by entering a new, valid, residue name. If several rings are being attached to copies of the structure, new residue names can also be separated by commas, each corresponding to the new ring.
Finally, click the 'put a ring on current selection' button to add a ring to the structure.
Rings from the library can be dropped into existing structures or a new model by selecting a structure from the drop-down menu and clicking the 'place in' button.
Switch to the 'change element' tab on the tool.
Select an atom. By default, the element is set to carbon. To change this, click the element symbol button and select a new element on the periodic table. Select a VSEPR geometry from the drop-down menu. Checking 'adjust bond lengths' will set the length of bonds to this atom to a value that is appropriate for a single bond.
Change the element of selected atoms by clicking the 'change selected elements' button. Note that the element of adjacent atoms cannot be changed simultaneously.
New atoms can be dropped into existing structures or used to start a new structure. Select the structure on the drop-down menu and press the 'place in' button.
Selected atoms can also be deleted by clicking the 'delete selected atoms' button.
- ChimeraX's Build Structure tool
- SEQCROW's
substitutecommand - SEQCROW's
fuseRingcommand - SEQCROW's Add to Personal Library tool